Pre-processing of the data

## -Validating
## --Non MAF specific values in Variant_Classification column:
##   Unknown
## --Non MAF specific values in Variant_Type column:
##   MNP
## -Silent variants: 5466 
## -Summarizing
## --Possible FLAGS among top ten genes:
##   TTN
##   MUC16
##   USH2A
##   FLG
## -Processing clinical data
## --Missing clinical data
## -Finished in 1.359s elapsed (1.307s cpu)

MAF object

## An object of class  MAF 
##                    ID summary    Mean Median
##  1:        NCBI_Build      NA      NA     NA
##  2:            Center      NA      NA     NA
##  3:           Samples      57      NA     NA
##  4:            nGenes    7980      NA     NA
##  5:   Frame_Shift_Del     594  10.421      5
##  6:   Frame_Shift_Ins     140   2.456      1
##  7:      In_Frame_Del     134   2.351      1
##  8:      In_Frame_Ins      21   0.368      0
##  9: Missense_Mutation   13065 229.211    104
## 10: Nonsense_Mutation    1099  19.281      7
## 11:  Nonstop_Mutation      19   0.333      0
## 12:       Splice_Site       3   0.053      0
## 13:             total   15075 264.474    120
## Warning in titv(maf = maf, useSyn = TRUE, plot = FALSE): Non standard Ti/Tv
## class: 581TRUE

Oncoplots

Transition and Transversions

## Warning in titv(maf = laml, plot = FALSE, useSyn = TRUE): Non standard Ti/Tv
## class: 581TRUE

KRAS mutations

## 2 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.
##    HGNC refseq.ID protein.ID aa.length
## 1: KRAS NM_004985  NP_004976       188
## 2: KRAS NM_033360  NP_203524       189
## Using longer transcript NM_033360 for now.

## Assuming protein change information are stored under column AAChange. Use argument AACol to override if necessary.
## 2 transcripts available. Use arguments refSeqID or proteinID to manually specify tx name.
##    HGNC refseq.ID protein.ID aa.length
## 1: KRAS NM_004985  NP_004976       188
## 2: KRAS NM_033360  NP_203524       189
## Using longer transcript NM_033360 for now.

Compare mutation load against TCGA cohorts

## Warning in FUN(X[[i]], ...): Removed 0 samples with zero mutations.
## Performing pairwise t-test for differences in mutation burden..

Somatic Interactions

##       gene1   gene2       pValue  oddsRatio 00 11 01 10              Event
##   1: ERICH3   ZFHX4 1.003317e-05 32.8729364 41  9  5  2       Co_Occurence
##   2:   TP53   CSMD3 1.018220e-05 19.8465407 36 12  5  4       Co_Occurence
##   3: PCDH15   OBSCN 1.388620e-05 33.4543447 43  8  3  3       Co_Occurence
##   4:  CSMD3   ZFHX4 1.653064e-05 20.7539826 37 11  3  6       Co_Occurence
##   5:  MUC16 CACNA1E 4.762487e-05 21.3778707 37 10  2  8       Co_Occurence
##  ---                                                                      
## 296:   RELN   CSMD1 1.000000e+00  0.9150065 37  2  9  9 Mutually_Exclusive
## 297:   RYR3   OBSCN 1.000000e+00  1.0545483 38  2  9  8       Co_Occurence
## 298:   RYR3  PCDH15 1.000000e+00  1.0545483 38  2  9  8       Co_Occurence
## 299:   RYR3 CCDC168 1.000000e+00  1.2143645 39  2  8  8       Co_Occurence
## 300:   VCAN   MUC12 1.000000e+00  1.2143645 39  2  8  8       Co_Occurence
##                pair event_ratio
##   1:  ERICH3, ZFHX4         9/7
##   2:    CSMD3, TP53        12/9
##   3:  OBSCN, PCDH15         8/6
##   4:   CSMD3, ZFHX4        11/9
##   5: CACNA1E, MUC16       10/10
##  ---                           
## 296:    CSMD1, RELN        2/18
## 297:    OBSCN, RYR3        2/17
## 298:   PCDH15, RYR3        2/17
## 299:  CCDC168, RYR3        2/16
## 300:    MUC12, VCAN        2/16

Detecting cancer driver genes based on positional clustering

## Warning in oncodrive(maf = laml, AACol = "Protein_Change", minMut = 5,
## pvalMethod = "zscore"): Oncodrive has been superseeded by OncodriveCLUSTL. See
## http://bg.upf.edu/group/projects/oncodrive-clust.php
## Estimating background scores from synonymous variants..
## Not enough genes to build background. Using predefined values. (Mean = 0.279; SD = 0.13)
## Estimating cluster scores from non-syn variants..
## 
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## Comapring with background model and estimating p-values..
## Done !
Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins Missense_Mutation Nonsense_Mutation Nonstop_Mutation Splice_Site total MutatedSamples AlteredSamples clusters muts_in_clusters clusterScores protLen zscore pval fdr fract_muts_in_clusters
KRAS 0 0 0 0 24 0 0 0 24 24 24 2 22 0.9044628 189 4.8112522 0.0000007 0.0000180 0.9166667
EPB41L3 0 0 0 0 5 0 0 0 5 4 4 2 4 0.8000000 1087 4.0076923 0.0000307 0.0003679 0.8000000
EGFR 0 0 7 1 9 0 0 0 17 12 12 2 11 0.5311959 1210 1.9399684 0.0261918 0.2095341 0.6470588
ATR 1 0 0 0 3 1 0 0 5 4 4 1 2 0.4000000 2644 0.9307692 0.1759865 0.4692973 0.4000000
C8A 1 0 0 0 4 0 0 0 5 4 4 1 2 0.4000000 584 0.9307692 0.1759865 0.4692973 0.4000000
DLGAP2 1 0 0 0 4 0 0 0 5 4 4 1 2 0.4000000 975 0.9307692 0.1759865 0.4692973 0.4000000

Clinical enrichment analysis

## Sample size per factor in Hist_predominant:
## 
##          acinar         lepidic  micropapillary mucinous acinar       papillary 
##              26               1               7               3               6 
##           solid 
##              14
## Sample size per factor in X8th_ed_path_stage:
## 
##  Stage IA1  Stage IA2  Stage IA3   Stage IB  Stage IIA  Stage IIB Stage IIIA 
##          5          8         12          8         12         10          1 
## Stage IIIB 
##          1
## Sample size per factor in n_op1:
## 
## agg ind 
##  44  13
## Sample size per factor in n_op2:
## 
## agg ind int 
##  36   5  16
##     Hugo_Symbol         Group1 Group2 n_mutated_group1 n_mutated_group2
##  1:       KNDC1          solid   Rest          7 of 14          1 of 43
##  2:       CSMD3         acinar   Rest          2 of 26         15 of 31
##  3:       DNAH8          solid   Rest          6 of 14          2 of 43
##  4:     CACNA1C          solid   Rest          5 of 14          1 of 43
##  5:       SPTA1         acinar   Rest          0 of 26          9 of 31
##  6:       MUC5B micropapillary   Rest           4 of 7          3 of 50
##  7:        FAT3          solid   Rest          6 of 14          3 of 43
##  8:       SPTA1          solid   Rest          6 of 14          3 of 43
##  9:      PAPPA2 micropapillary   Rest           4 of 7          4 of 50
## 10:      BRINP3         acinar   Rest          0 of 26          8 of 31
## 11:       ZFHX4 micropapillary   Rest           5 of 7          9 of 50
## 12:        LRP2          solid   Rest          5 of 14          2 of 43
## 13:       STAB2          solid   Rest          5 of 14          2 of 43
## 14:      ADGRL3         acinar   Rest          1 of 26         10 of 31
## 15:       OBSCN         acinar   Rest          1 of 26         10 of 31
## 16:        PCLO micropapillary   Rest           4 of 7          5 of 50
## 17:     CCDC168          solid   Rest          6 of 14          4 of 43
## 18:       ZFHX4         acinar   Rest          2 of 26         12 of 31
## 19:     PKHD1L1         acinar   Rest          0 of 26          7 of 31
## 20:        TP53          solid   Rest          8 of 14          8 of 43
## 21:       USH2A micropapillary   Rest           5 of 7         11 of 50
## 22:     CCDC168         acinar   Rest          1 of 26          9 of 31
## 23:       MUC12         acinar   Rest          1 of 26          9 of 31
## 24:      MALRD1          solid   Rest          5 of 14          3 of 43
## 25:       PRDM9          solid   Rest          5 of 14          3 of 43
## 26:         ZAN          solid   Rest          5 of 14          3 of 43
## 27:       CSMD3          solid   Rest          8 of 14          9 of 43
## 28:      ERICH3          solid   Rest          6 of 14          5 of 43
## 29:       OBSCN          solid   Rest          6 of 14          5 of 43
## 30:      PLXNA4 micropapillary   Rest           3 of 7          3 of 50
## 31:    TMEM132B micropapillary   Rest           3 of 7          3 of 50
## 32:       CSMD3 micropapillary   Rest           5 of 7         12 of 50
## 33:       MUC16         acinar   Rest          4 of 26         14 of 31
## 34:         TTN          solid   Rest          8 of 14         10 of 43
## 35:     CACNA1C         acinar   Rest          0 of 26          6 of 31
## 36:       TENM3         acinar   Rest          0 of 26          6 of 31
## 37:        MYH6         acinar   Rest          0 of 26          6 of 31
## 38:       TSHZ3         acinar   Rest          0 of 26          6 of 31
## 39:      ZNF479         acinar   Rest          0 of 26          6 of 31
## 40:      MUC5AC         acinar   Rest          0 of 26          6 of 31
## 41:        EGFR         acinar   Rest          9 of 26          3 of 31
## 42:       ZFHX4          solid   Rest          7 of 14          7 of 43
## 43:         FLG          solid   Rest          7 of 14          7 of 43
## 44:      COL6A5          solid   Rest          4 of 14          2 of 43
## 45:      MROH2B          solid   Rest          4 of 14          2 of 43
## 46:       SALL3          solid   Rest          4 of 14          2 of 43
## 47:       UNC79          solid   Rest          4 of 14          2 of 43
## 48:        ANK3          solid   Rest          4 of 14          2 of 43
## 49:       TENM3          solid   Rest          4 of 14          2 of 43
## 50:        MYH6          solid   Rest          4 of 14          2 of 43
## 51:       TSHZ3          solid   Rest          4 of 14          2 of 43
## 52:      ZNF479          solid   Rest          4 of 14          2 of 43
## 53:       BECN2          solid   Rest          4 of 14          2 of 43
## 54:      EGFLAM          solid   Rest          4 of 14          2 of 43
## 55:       GRIK4          solid   Rest          4 of 14          2 of 43
## 56:      GRIN2B          solid   Rest          4 of 14          2 of 43
## 57:      MUC5AC          solid   Rest          4 of 14          2 of 43
## 58:      PKD1L1          solid   Rest          4 of 14          2 of 43
## 59:      THSD7A          solid   Rest          4 of 14          2 of 43
## 60:      VPS13B         acinar   Rest          1 of 26          8 of 31
## 61:      ZNF536         acinar   Rest          1 of 26          8 of 31
## 62:    ADAMTS20         acinar   Rest          1 of 26          8 of 31
## 63:      COL6A3         acinar   Rest          1 of 26          8 of 31
## 64:        FAT4         acinar   Rest          1 of 26          8 of 31
## 65:        DGKI         acinar   Rest          1 of 26          8 of 31
## 66:       KEAP1      papillary   Rest           3 of 6          5 of 51
## 67:      CTNND2          solid   Rest          5 of 14          4 of 43
## 68:       HMCN2          solid   Rest          5 of 14          4 of 43
## 69:      VPS13B          solid   Rest          5 of 14          4 of 43
## 70:      COL6A3          solid   Rest          5 of 14          4 of 43
## 71:        DGKI          solid   Rest          5 of 14          4 of 43
## 72:     PKHD1L1 micropapillary   Rest           3 of 7          4 of 50
## 73:       MUC3A micropapillary   Rest           3 of 7          4 of 50
## 74:    ADAMTS20      papillary   Rest           3 of 6          6 of 51
##     Hugo_Symbol         Group1 Group2 n_mutated_group1 n_mutated_group2
##          p_value          OR      OR_low      OR_high        fdr
##  1: 9.112682e-05 37.84731092 3.991610776 1909.7571373 0.09240259
##  2: 1.095098e-03  0.09270694 0.009091654    0.4818028 0.45517130
##  3: 1.732188e-03 14.31983532 2.102947979  169.6342488 0.45517130
##  4: 2.455037e-03 21.57334820 2.079276821 1120.1578249 0.45517130
##  5: 2.588198e-03  0.00000000 0.000000000    0.4975338 0.45517130
##  6: 2.693321e-03 18.64859301 2.157445266  205.3771129 0.45517130
##  7: 4.478455e-03  9.44023459 1.627744533   70.9908140 0.45617315
##  8: 4.478455e-03  9.44023459 1.627744533   70.9908140 0.45617315
##  9: 5.132332e-03 13.99157827 1.741541318  135.0781052 0.45617315
## 10: 5.719520e-03  0.00000000 0.000000000    0.5969768 0.45617315
## 11: 7.339149e-03 10.72219374 1.479698932  129.6610724 0.45617315
## 12: 7.339149e-03 10.72219374 1.479698932  129.6610724 0.45617315
## 13: 7.339149e-03 10.72219374 1.479698932  129.6610724 0.45617315
## 14: 7.643077e-03  0.08711217 0.001868086    0.7010832 0.45617315
## 15: 7.643077e-03  0.08711217 0.001868086    0.7010832 0.45617315
## 16: 8.795827e-03 11.12131460 1.450631913  100.2633539 0.45617315
## 17: 9.627704e-03  6.97278498 1.317966294   42.3117118 0.45617315
## 18: 1.183212e-02  0.13643416 0.013302517    0.7247362 0.45617315
## 19: 1.243401e-02  0.00000000 0.000000000    0.7319136 0.45617315
## 20: 1.332626e-02  5.61133142 1.304302871   26.3072872 0.45617315
## 21: 1.483259e-02  8.43880117 1.188600998  100.1107290 0.45617315
## 22: 1.553126e-02  0.10115754 0.002152104    0.8305514 0.45617315
## 23: 1.553126e-02  0.10115754 0.002152104    0.8305514 0.45617315
## 24: 1.668408e-02  7.06058247 1.141058515   54.1810940 0.45617315
## 25: 1.668408e-02  7.06058247 1.141058515   54.1810940 0.45617315
## 26: 1.668408e-02  7.06058247 1.141058515   54.1810940 0.45617315
## 27: 1.746912e-02  4.86689286 1.152659066   22.2327873 0.45617315
## 28: 1.817327e-02  5.47738734 1.099107756   29.3982865 0.45617315
## 29: 1.817327e-02  5.47738734 1.099107756   29.3982865 0.45617315
## 30: 2.011483e-02 10.82851627 1.099157081  113.1606494 0.45617315
## 31: 2.011483e-02 10.82851627 1.099157081  113.1606494 0.45617315
## 32: 2.020202e-02  7.57039468 1.074438284   89.3371864 0.45617315
## 33: 2.242488e-02  0.22678515 0.045851352    0.8955596 0.45617315
## 34: 2.465971e-02  4.26767929 1.026024439   19.0908509 0.45617315
## 35: 2.663427e-02  0.00000000 0.000000000    0.9251826 0.45617315
## 36: 2.663427e-02  0.00000000 0.000000000    0.9251826 0.45617315
## 37: 2.663427e-02  0.00000000 0.000000000    0.9251826 0.45617315
## 38: 2.663427e-02  0.00000000 0.000000000    0.9251826 0.45617315
## 39: 2.663427e-02  0.00000000 0.000000000    0.9251826 0.45617315
## 40: 2.663427e-02  0.00000000 0.000000000    0.9251826 0.45617315
## 41: 2.701395e-02  4.80038030 1.014565736   31.4180299 0.45617315
## 42: 2.720528e-02  4.96068258 1.111485949   23.4449711 0.45617315
## 43: 2.720528e-02  4.96068258 1.111485949   23.4449711 0.45617315
## 44: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 45: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 46: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 47: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 48: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 49: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 50: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 51: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 52: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 53: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 54: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 55: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 56: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 57: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 58: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 59: 2.736401e-02  7.79869341 0.966262240   97.7488781 0.45617315
## 60: 3.077009e-02  0.11869263 0.002499335    1.0004947 0.45617315
## 61: 3.077009e-02  0.11869263 0.002499335    1.0004947 0.45617315
## 62: 3.077009e-02  0.11869263 0.002499335    1.0004947 0.45617315
## 63: 3.077009e-02  0.11869263 0.002499335    1.0004947 0.45617315
## 64: 3.077009e-02  0.11869263 0.002499335    1.0004947 0.45617315
## 65: 3.077009e-02  0.11869263 0.002499335    1.0004947 0.45617315
## 66: 3.077679e-02  8.60369168 0.912225806   84.1612977 0.45617315
## 67: 3.194112e-02  5.21145581 0.921403533   32.2038762 0.45617315
## 68: 3.194112e-02  5.21145581 0.921403533   32.2038762 0.45617315
## 69: 3.194112e-02  5.21145581 0.921403533   32.2038762 0.45617315
## 70: 3.194112e-02  5.21145581 0.921403533   32.2038762 0.45617315
## 71: 3.194112e-02  5.21145581 0.921403533   32.2038762 0.45617315
## 72: 3.318096e-02  8.08275241 0.882293807   71.9160436 0.46089718
## 73: 3.318096e-02  8.08275241 0.882293807   71.9160436 0.46089718
## 74: 4.412238e-02  7.08910525 0.774798722   66.6306331 0.54820713
##          p_value          OR      OR_low      OR_high        fdr

Oncogenic Signaling Pathways

##        Pathway  N n_affected_genes fraction_affected Mutated_samples
##  1:       NRF2  3                1         0.3333333               8
##  2:       TP53  6                4         0.6666667              21
##  3:   TGF-Beta  7                5         0.7142857               4
##  4:        MYC 13                6         0.4615385              10
##  5: Cell_Cycle 15                7         0.4666667               6
##  6:       PI3K 29               14         0.4827586              17
##  7:      Hippo 38               23         0.6052632              30
##  8:        WNT 68               30         0.4411765              22
##  9:      NOTCH 71               38         0.5352113              29
## 10:    RTK-RAS 85               50         0.5882353              47
##     Fraction_mutated_samples
##  1:               0.14035088
##  2:               0.36842105
##  3:               0.07017544
##  4:               0.17543860
##  5:               0.10526316
##  6:               0.29824561
##  7:               0.52631579
##  8:               0.38596491
##  9:               0.50877193
## 10:               0.82456140

Clinical enrichment analysis (by aggressiveness)

## Sample size per factor in n_op2:
## 
## agg ind int 
##  36   5  16
##     Hugo_Symbol Group1 Group2 n_mutated_group1 n_mutated_group2    p_value
##  1:      CTNND2    agg   Rest          9 of 36          0 of 21 0.01945423
##  2:        APOB    agg   Rest          8 of 36          0 of 21 0.02096930
##  3:    ADAMTS12    agg   Rest          8 of 36          0 of 21 0.02096930
##  4:       PRDM9    agg   Rest          8 of 36          0 of 21 0.02096930
##  5:       NPAP1    agg   Rest          8 of 36          0 of 21 0.02096930
##  6:      SORCS1    agg   Rest          8 of 36          0 of 21 0.02096930
##  7:       CSMD3    int   Rest          1 of 16         16 of 41 0.02216306
##  8:      ADGRB3    agg   Rest          7 of 36          0 of 21 0.03940250
##  9:       DCHS2    agg   Rest          7 of 36          0 of 21 0.03940250
## 10:      LRRTM4    agg   Rest          7 of 36          0 of 21 0.03940250
## 11:       PTPRC    agg   Rest          7 of 36          0 of 21 0.03940250
## 12:      UNC13B    agg   Rest          7 of 36          0 of 21 0.03940250
## 13:     CACNA1E    agg   Rest         11 of 36          1 of 21 0.03985523
## 14:       OBSCN    agg   Rest         10 of 36          1 of 21 0.04113546
## 15:      CTNND2    int   Rest          0 of 16          9 of 41 0.04953378
## 16:     CNTNAP4    int   Rest          0 of 16          9 of 41 0.04953378
##            OR      OR_low     OR_high      fdr
##  1:       Inf 1.328554223         Inf 0.946737
##  2:       Inf 1.114985573         Inf 0.946737
##  3:       Inf 1.114985573         Inf 0.946737
##  4:       Inf 1.114985573         Inf 0.946737
##  5:       Inf 1.114985573         Inf 0.946737
##  6:       Inf 1.114985573         Inf 0.946737
##  7: 0.1073769 0.002336399   0.8338525 0.946737
##  8:       Inf 0.915476308         Inf 0.946737
##  9:       Inf 0.915476308         Inf 0.946737
## 10:       Inf 0.915476308         Inf 0.946737
## 11:       Inf 0.915476308         Inf 0.946737
## 12:       Inf 0.915476308         Inf 0.946737
## 13: 8.5420267 1.073296253 396.5505636 0.946737
## 14: 7.4804942 0.924818360 349.5846230 0.946737
## 15: 0.0000000 0.000000000   1.1814139 0.946737
## 16: 0.0000000 0.000000000   1.1814139 0.946737

# Comparing groups (separate MAFs)

## -subsetting by clinical data..
## --5 samples meet the clinical query
## -subsetting by clinical data..
## --16 samples meet the clinical query
## -subsetting by clinical data..
## --36 samples meet the clinical query

Indolent vs Aggressive

Hugo_Symbol Indolent Aggressive pval or ci.up ci.low adjPval
TTN 0 14 0.1464629 0.0000000 2.018898 0.0000000 1
DNAH5 2 5 0.1955036 3.9411355 44.918622 0.2672986 1
EGFR 2 5 0.1955036 3.9411355 44.918622 0.2672986 1
RYR3 2 5 0.1955036 3.9411355 44.918622 0.2672986 1
ANK2 2 6 0.2464672 3.2097811 35.157183 0.2234139 1
CACNA1E 0 11 0.2997646 0.0000000 2.956327 0.0000000 1
USH2A 0 11 0.2997646 0.0000000 2.956327 0.0000000 1
OBSCN 0 10 0.3102130 0.0000000 3.408577 0.0000000 1
RYR2 3 11 0.3169517 3.2975734 44.753434 0.3292036 1
ADAMTS12 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
APOB 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
MUC12 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
NPAP1 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
OVCH1 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
PCDH15 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
PCLO 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
PRDM9 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
RELN 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
SORCS1 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
ZNF536 0 8 0.5631694 0.0000000 4.703327 0.0000000 1
AHNAK2 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
ANK3 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
CACNA1C 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
COL6A5 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
CUBN 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
FBN2 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
HSPG2 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
KEAP1 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
MUC3A 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
MXRA5 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
NCKAP5 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
PEG3 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
PTPRD 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
SLITRK3 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
SPATA31D1 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
SPTBN4 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
TMEM132B 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
TRPC5 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
ZNF479 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
ZNF804A 1 5 0.5668096 1.5315061 20.682565 0.0262792 1
ADGRB3 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
CDH2 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
COL6A3 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
DCHS2 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
ICE1 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
LRRTM4 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
PAPPA2 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
PTPRC 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
RBM10 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
SLITRK2 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
UNC13B 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
VPS13B 0 7 0.5668096 0.0000000 5.678487 0.0000000 1
CTNND2 0 9 0.5681334 0.0000000 3.974876 0.0000000 1
ADGRL3 2 8 0.5801297 2.2779952 23.803332 0.1638122 1
XIRP2 2 9 0.5977371 1.9626143 20.205003 0.1426448 1
FLG 2 10 0.6196787 1.7082681 17.388165 0.1252037 1
MUC16 1 14 0.6357076 0.4008352 4.623071 0.0074587 1
LRP1B 2 11 0.6448149 1.4990570 15.123036 0.1105846 1
ABCA13 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
ADAMTS20 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
BRINP3 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
CACNA1I 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
CADM3 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
CCDC168 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
CSMD2 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
CSMD3 2 14 1.0000000 1.0464010 10.385608 0.0781803 1
DGKI 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
DNAH8 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
EGFLAM 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
EPHA3 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
EYS 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
FAT2 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
FAT3 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
FAT4 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
FSIP2 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
HMCN1 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
HMCN2 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
IGFN1 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
KCNT2 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
KIAA1109 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
KNDC1 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
LRP2 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
MALRD1 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
MGAM 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
MGAM2 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
MROH2B 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
MTUS2 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
MUC17 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
MUC5B 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
MYH2 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
OTOGL 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
PKHD1L1 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
PXDNL 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
SI 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
SPTA1 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
STAB2 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
TENM3 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
THSD7A 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
TP53 1 11 1.0000000 0.5753117 6.760275 0.0105936 1
TPTE 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
TSHZ3 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
UNC79 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
VCAN 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
WDFY4 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
ZFHX4 1 12 1.0000000 0.5076059 5.918500 0.0093877 1
ZFPM2 1 7 1.0000000 1.0348233 12.930454 0.0184306 1
ZNF423 1 6 1.0000000 1.2428269 16.023515 0.0217935 1
ZNF729 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
ZNF831 0 6 1.0000000 0.0000000 7.048622 0.0000000 1
ADGRV1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ALPK1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ALPK3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ARID1A 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ARPP21 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ASB15 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ASTN1 1 10 1.0000000 0.6563176 7.788950 0.0120189 1
ASTN2 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ASXL3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ATP1A4 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
BIRC6 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
C6orf132 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CA9 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CACNA2D1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CD163 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CDH12 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CFHR5 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CNTNAP4 1 8 1.0000000 0.8777738 10.727789 0.0158209 1
CNTNAP5 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
COL12A1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
COL22A1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
COL2A1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
COL3A1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
COL4A5 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CRYBG2 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
CSMD1 1 9 1.0000000 0.7550003 9.074672 0.0137296 1
DGKB 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
DNAH10 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
DNAH11 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
DNAH3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
DNAH7 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
DST 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
EDIL3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ERICH3 1 9 1.0000000 0.7550003 9.074672 0.0137296 1
FCGBP 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
KCNH7 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
KCP 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
KRAS 2 15 1.0000000 0.9348824 9.249026 0.0700072 1
KRBA1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
LAMA1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
LRRC7 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
MROH2A 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
MYH4 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
MYH6 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
NAV3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
NBAS 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
NEB 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
NELL1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
NRXN1 1 10 1.0000000 0.6563176 7.788950 0.0120189 1
NXF5 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
OR2T2 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
PKD1L1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
PLXNA4 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
POTEA 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
POU3F3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
PPFIA2 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
RIMBP2 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
RP1L1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
RYR1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
SALL3 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
SCN3A 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
TIAM1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
TMEM132C 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
TNN 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ZEB1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
ZIC1 0 5 1.0000000 0.0000000 9.119767 0.0000000 1
Cohort SampleSize
Indolent 5
Aggressive 36

Indolent+Intermediate vs Aggressive

## -subsetting by clinical data..
## --21 samples meet the clinical query
## -subsetting by clinical data..
## --36 samples meet the clinical query
Hugo_Symbol Indolent + Int Aggressive pval or ci.up ci.low adjPval
CTNND2 0 9 0.0194542 0.0000000 0.7526979 0.0000000 0.3846968
ADAMTS12 0 8 0.0209693 0.0000000 0.8968726 0.0000000 0.3846968
APOB 0 8 0.0209693 0.0000000 0.8968726 0.0000000 0.3846968
NPAP1 0 8 0.0209693 0.0000000 0.8968726 0.0000000 0.3846968
PRDM9 0 8 0.0209693 0.0000000 0.8968726 0.0000000 0.3846968
SORCS1 0 8 0.0209693 0.0000000 0.8968726 0.0000000 0.3846968
ADGRB3 0 7 0.0394025 0.0000000 1.0923276 0.0000000 0.3846968
DCHS2 0 7 0.0394025 0.0000000 1.0923276 0.0000000 0.3846968
LRRTM4 0 7 0.0394025 0.0000000 1.0923276 0.0000000 0.3846968
PTPRC 0 7 0.0394025 0.0000000 1.0923276 0.0000000 0.3846968
UNC13B 0 7 0.0394025 0.0000000 1.0923276 0.0000000 0.3846968
CACNA1E 1 11 0.0398552 0.1170682 0.9317092 0.0025217 0.3846968
OBSCN 1 10 0.0411355 0.1336810 1.0812934 0.0028605 0.3846968
ZFHX4 2 12 0.0584136 0.2156646 1.1514147 0.0209878 0.3846968
CSMD3 3 14 0.0725792 0.2677393 1.1764364 0.0427106 0.3846968
CSMD2 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
EGFLAM 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
EPHA3 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
IGFN1 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
MGAM2 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
MROH2B 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
PXDNL 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
TENM3 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
THSD7A 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
TPTE 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
TSHZ3 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
UNC79 0 6 0.0753583 0.0000000 1.3720598 0.0000000 0.3846968
EGFR 7 5 0.1018339 3.0333470 14.4652194 0.6913165 0.3846968
CNTNAP4 1 8 0.1331558 0.1792817 1.5206016 0.0037643 0.3846968
PCLO 1 8 0.1331558 0.1792817 1.5206016 0.0037643 0.3846968
ZNF536 1 8 0.1331558 0.1792817 1.5206016 0.0037643 0.3846968
ALPK1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
ARPP21 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
ASB15 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
ATP1A4 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
C6orf132 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
CA9 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
CACNA2D1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
CD163 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
CDH12 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
CFHR5 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
CNTNAP5 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
COL12A1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
COL22A1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
COL2A1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
COL4A5 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
DGKB 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
DNAH10 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
DNAH3 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
DST 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
EDIL3 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
KCP 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
KRBA1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
LRRC7 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
MROH2A 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
MYH4 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
NEB 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
NELL1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
NXF5 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
OR2T2 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
POTEA 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
POU3F3 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
PPFIA2 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
RIMBP2 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
RYR1 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
SCN3A 0 5 0.1463543 0.0000000 1.8040200 0.0000000 0.3846968
MUC16 4 14 0.1486329 0.3760077 1.4955896 0.0760950 0.3846968
TTN 4 14 0.1486329 0.3760077 1.4955896 0.0760950 0.3846968
ASTN1 2 10 0.1773045 0.2792342 1.5390316 0.0267534 0.4457941
NRXN1 2 10 0.1773045 0.2792342 1.5390316 0.0267534 0.4457941
CSMD1 2 9 0.1854077 0.3215125 1.8126233 0.0305038 0.4532188
ERICH3 2 9 0.1854077 0.3215125 1.8126233 0.0305038 0.4532188
LRP1B 3 11 0.2137720 0.3848555 1.7530604 0.0602898 0.4797555
CDH2 1 7 0.2356734 0.2117815 1.8614334 0.0043859 0.4797555
DNAH8 1 7 0.2356734 0.2117815 1.8614334 0.0043859 0.4797555
PAPPA2 1 7 0.2356734 0.2117815 1.8614334 0.0043859 0.4797555
SLITRK2 1 7 0.2356734 0.2117815 1.8614334 0.0043859 0.4797555
WDFY4 1 7 0.2356734 0.2117815 1.8614334 0.0043859 0.4797555
ZFPM2 1 7 0.2356734 0.2117815 1.8614334 0.0043859 0.4797555
CADM3 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
HMCN1 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
KCNT2 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
LRP2 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
MGAM 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
MUC5B 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
PKHD1L1 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
STAB2 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
ZNF729 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
ZNF831 1 6 0.2426036 0.2550261 2.3544444 0.0051855 0.4797555
TENM1 5 4 0.2663924 2.4572820 14.2260245 0.4589171 0.5209451
MUC12 2 8 0.2952934 0.3742905 2.1728706 0.0350259 0.5649091
OVCH1 2 8 0.2952934 0.3742905 2.1728706 0.0350259 0.5649091
RYR2 9 11 0.3973204 1.6882593 5.9817925 0.4778288 0.6190044
ALPK3 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
ANK3 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
ARID1A 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
ASTN2 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
CACNA1C 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
COL3A1 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
COL6A5 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
CRYBG2 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
FCGBP 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
KCNH7 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
MYH6 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
NBAS 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
PKD1L1 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
PLXNA4 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
RP1L1 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
SALL3 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
TMEM132B 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
ZEB1 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
ZIC1 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
ZNF479 1 5 0.3974290 0.3154090 3.1267166 0.0062521 0.6190044
COL6A3 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
DGKI 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
ICE1 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
KIAA1109 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
RBM10 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
SPTA1 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
VPS13B 2 7 0.4612482 0.4419318 2.6677534 0.0406451 0.6764973
RYR3 5 5 0.4729422 1.9139979 9.7078377 0.3795817 0.6879159
XIRP2 3 9 0.5037717 0.5057722 2.4044101 0.0775279 0.7267527
FLG 4 10 0.5376305 0.6168900 2.5968468 0.1211591 0.7692925
ABCA13 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
BRINP3 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
CACNA1I 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
EYS 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
FSIP2 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
KNDC1 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
MALRD1 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
MTUS2 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
MYH2 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
SI 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
ZNF423 2 6 0.6965651 0.5318590 3.3878174 0.0478025 0.9148914
ADGRL3 3 8 0.7292230 0.5886169 2.8863169 0.0888244 0.9243717
PCDH15 3 8 0.7292230 0.5886169 2.8863169 0.0888244 0.9243717
RELN 3 8 0.7292230 0.5886169 2.8863169 0.0888244 0.9243717
CCDC168 3 7 0.7300435 0.6948259 3.5505425 0.1028103 0.9243717
VCAN 3 7 0.7300435 0.6948259 3.5505425 0.1028103 0.9243717
TP53 5 11 0.7617846 0.7144253 2.7724814 0.1628221 0.9508801
USH2A 5 11 0.7617846 0.7144253 2.7724814 0.1628221 0.9508801
DNAH5 3 5 1.0000000 1.0327617 6.0589848 0.1433700 1.0000000
KEAP1 3 5 1.0000000 1.0327617 6.0589848 0.1433700 1.0000000
KRAS 9 15 1.0000000 1.0490724 3.5504102 0.3047852 1.0000000
LAMA1 3 5 1.0000000 1.0327617 6.0589848 0.1433700 1.0000000
MXRA5 3 5 1.0000000 1.0327617 6.0589848 0.1433700 1.0000000
SPATA31D1 3 5 1.0000000 1.0327617 6.0589848 0.1433700 1.0000000
ADAMTS20 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
ADGRV1 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
AHNAK2 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
ANK2 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
ASXL3 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
BIRC6 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
CUBN 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
DNAH11 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
DNAH7 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
FAT2 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
FAT3 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
FAT4 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
FBN2 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
HMCN2 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
HSPG2 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
MUC17 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
MUC3A 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
NAV3 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
NCKAP5 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
OTOGL 3 6 1.0000000 0.8359613 4.5204359 0.1203777 1.0000000
PEG3 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
PTPRD 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
SLITRK3 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
SPTBN4 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
TIAM1 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
TMEM132C 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
TNN 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
TRPC5 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
ZNF804A 2 5 1.0000000 0.6573022 4.5246559 0.0572104 1.0000000
Cohort SampleSize
Indolent + Int 21
Aggressive 36